User: shintzen

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shintzen10
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Posts by shintzen

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RNA-SeQC v1.1.8 transcript_id attribute was not found
... Hi, I am running RNA-SeQC on some files with Ensembl. I know Ensembl format is "malformed" to this tool but I have followed the args to try to provide a different type of id and I still am not making progress. java -jar RNA-SeQC_v1.1.8.jar -ttype "gene_biotype" -r rna-seq/hg38_nochr.fa -t rna- ...
qc rna-seq written 27 days ago by shintzen10
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Comment: C: MSTRGs are plaguing my RNA-Seq analysis
... From what I read I thought the same as you described where it is an expected issue, and just needed some external confirmation that there was nothing super obvious that I was missing as far as analysis and settings. Thanks ...
written 9 weeks ago by shintzen10
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MSTRGs are plaguing my RNA-Seq analysis
... Hi, I have been trying to run RNA seq analysis on some paired end data. I have aligned on HISAT2, and run Stringtie, Stringtie Merge and then Stringtie again. To do the analysis I am using: grch38_tran.tar.gz - https://ccb.jhu.edu/software/hisat2/index.shtml Homo_sapiens.GRCh38.84.gtf - ftp://ftp.en ...
alignment rna-seq written 9 weeks ago by shintzen10 • updated 9 weeks ago by andrew.j.skelton735.5k

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